This journal entry is due on Wednesday, November 2 at midnight PDT(Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).

Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.

Link to your journal entry from your user page.

Link back from your journal entry to your user page.

Link to this assignment from your journal entry.

Don't forget to add the "BIOL368/F11" category to the end of your wiki page.

HIV Structure Redux

Pick two amino acid substitutions (two different positions) that you found in your HIV Structure Project. Use StarBiochem or Cn3D to locate those amino acids on the structure (either from Kwong or Stanfield).

Take a screenshot showing a view that shows the amino acid in question (one screenshot per amino acid). Save your screenshot in a PowerPoint slide and use an arrow or circle to point to the amino acid.

Interpret whether the amino acid is on the surface, buried, or at an interface with another protein, and whether the substitution should affect the function.

Answer the following Discovery Questions from Chapter 4

Number 5 from p. 110: Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.

Number 6b. from p. 110: Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6, determine the color for each ratio in Figure 4.7b.

Number 7 from p. 110: Were any of the genes in Figure 4.7b transcribed similarly?

Number 9 from p. 118: Why would most spots be yellow at the first time point?

Number 10 p. 118 Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).

Number 11 from p. 120: Why would TCA cycle genes be induced if the glucose supply is running out?

Number 12 from p. 120: What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

Number 13 from p. 121: Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?

Number 14 from p. 121: What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?

Number 15 from p. 121: Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?

Number 16 from p. 121: What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?

Finding a Journal Club Article/Microarray Dataset

Next week you will begin the DNA Microarray Project by preparing for your next Journal Club presentation that will take place in Week 12. You will work in groups of 2 or 3 on this project. Groups are:

Chris, Nicki - Mycobacterium smegmatis

Isaiah, Sam

Alex, Bobby, Zeb - Staphylococcus aureus MRSA25

You may choose to work ahead towards this presentation by finding your Journal Club article and corresponding microarray dataset with which you will perform your project. Your task is to find a published microarray dataset that measures gene expression from one of the following species:

Saccharomyces cerevisiae (yeast)

Escherichia coli K12

Helicobacter pylori

Mycobacterium smegmatis

Mycobacterium tuberculosis

Plasmodium falciparum

Pseudomonas aerugenosa

Salmonella typhimurium

Staphylococcus aureus MRSA252

Vibrio cholerae

Microarray data is not centrally located on the web. Some major sources are: